Index _ | A | B | C | D | E | F | G | K | L | M | N | O | P | R | S | T | V | W | Y _ __init__() (metadensity.config.MetadensityConfig method) (metadensity.metadensity.circRNA method) (metadensity.metadensity.eCLIP method) (metadensity.metadensity.lncRNA method) (metadensity.metadensity.Meta method) (metadensity.metadensity.Metadensity method) (metadensity.metadensity.Metagene method) (metadensity.metadensity.Metatruncate method) (metadensity.metadensity.miRNA method) (metadensity.metadensity.Protein_coding_gene method) (metadensity.metadensity.RNU method) (metadensity.metadensity.rRNA method) (metadensity.metadensity.snoRNA method) (metadensity.metadensity.STAMP method) (metadensity.metadensity.tRNA method) (metadensity.metadensity.vaultRNA method) (metadensity.metadensity.Window method) (metadensity.metadensity.YRNA method) (metadensity.pos_enrich.PosEnrichResult method) (metadensity.readdensity.Phastcon method) (metadensity.readdensity.ReadDensity method) (metadensity.shrink_region.Cluster method) A apply() (metadensity.metadensity.Meta method) auc_cum_dist() (in module metadensity.pos_enrich) auc_cum_wilcox() (in module metadensity.pos_enrich) auto_rbp_color() (in module metadensity.plotd) B beautify() (in module metadensity.plotd) build_full_cds() (metadensity.metadensity.Protein_coding_gene method) Build_many_metagene() (in module metadensity.metadensity) build_metagene() (metadensity.metadensity.Meta method) C calcaulte_grid_width() (in module metadensity.plotd) calculate_coverage() (metadensity.metadensity.eCLIP method) circRNA (class in metadensity.metadensity) Cluster (class in metadensity.shrink_region) concat_density() (metadensity.metadensity.Metagene method) concat_density_array() (metadensity.metadensity.Meta method) concat_multi_feature() (metadensity.metadensity.Metagene method) construct_distribution() (in module metadensity.pos_enrich) control_cluster() (in module metadensity.shrink_region) convolve() (metadensity.metadensity.Meta method) count_kmer() (in module metadensity.sequence) coverage (metadensity.metadensity.circRNA.self attribute) (metadensity.metadensity.lncRNA.self attribute) (metadensity.metadensity.Metagene.self attribute) (metadensity.metadensity.miRNA.self attribute) (metadensity.metadensity.Protein_coding_gene.self attribute) (metadensity.metadensity.RNU.self attribute) (metadensity.metadensity.rRNA.self attribute) (metadensity.metadensity.snoRNA.self attribute) (metadensity.metadensity.tRNA.self attribute) (metadensity.metadensity.vaultRNA.self attribute) (metadensity.metadensity.YRNA.self attribute) coverage_value() (metadensity.metadensity.Metagene method) create_downstream_feature() (metadensity.metadensity.Metagene method) create_feature() (metadensity.metadensity.Metagene method) create_upstream_feature() (metadensity.metadensity.Metagene method) D densities (metadensity.metadensity.circRNA.self attribute) (metadensity.metadensity.lncRNA.self attribute) (metadensity.metadensity.Metagene.self attribute) (metadensity.metadensity.miRNA.self attribute) (metadensity.metadensity.Protein_coding_gene.self attribute) (metadensity.metadensity.RNU.self attribute) (metadensity.metadensity.rRNA.self attribute) (metadensity.metadensity.snoRNA.self attribute) (metadensity.metadensity.tRNA.self attribute) (metadensity.metadensity.vaultRNA.self attribute) (metadensity.metadensity.YRNA.self attribute) Density (class in metadensity.readdensity) density_array_entropy() (in module metadensity.metadensity) E eCLIP (class in metadensity.metadensity) enough_coverage_transcript() (metadensity.metadensity.eCLIP method) enough_transcripts() (metadensity.metadensity.eCLIP method) enrich_by_thres() (in module metadensity.pos_enrich) enrich_plot() (in module metadensity.sequence) enrich_score() (metadensity.shrink_region.Cluster method) F featnames (metadensity.metadensity.circRNA.self attribute) (metadensity.metadensity.lncRNA.self attribute) (metadensity.metadensity.Metagene.self attribute) (metadensity.metadensity.miRNA.self attribute) (metadensity.metadensity.Protein_coding_gene.self attribute) (metadensity.metadensity.RNU.self attribute) (metadensity.metadensity.rRNA.self attribute) (metadensity.metadensity.snoRNA.self attribute) (metadensity.metadensity.tRNA.self attribute) (metadensity.metadensity.vaultRNA.self attribute) (metadensity.metadensity.YRNA.self attribute) fetch_reads() (in module metadensity.truncation) find_cluster() (in module metadensity.shrink_region) find_hairpin() (metadensity.metadensity.miRNA method) find_idr_transcript() (metadensity.metadensity.eCLIP method) from_config_file() (metadensity.config.MetadensityConfig method) from_dict() (metadensity.metadensity.Metagene class method) from_series() (metadensity.metadensity.eCLIP class method) G generate_axis() (in module metadensity.plotd) get_all_site_seq() (in module metadensity.kmer_from_read) get_average_feature() (metadensity.metadensity.Metagene method) get_cluster_seq() (in module metadensity.shrink_region) get_cmap() (in module metadensity.plotd) get_density_array() (metadensity.metadensity.Meta method) get_feature_density_array() (metadensity.metadensity.Meta method) get_interval_seq() (in module metadensity.sequence) get_metadensity() (metadensity.metadensity.Metadensity method) get_mismatch() (in module metadensity.truncation) get_raw_value() (metadensity.metadensity.Metagene method) get_truncation() (metadensity.metadensity.Metatruncate method) get_truncation_seq() (in module metadensity.sequence) get_value() (metadensity.metadensity.Metagene method) get_xticklabels() (in module metadensity.plotd) getRNAsequence() (in module metadensity.sequence) K kmer() (in module metadensity.sequence) kmer_rvalue() (in module metadensity.sequence) kmer_zscore() (in module metadensity.sequence) ks_all_pos() (in module metadensity.shape_from_read) KS_enrich() (in module metadensity.pos_enrich) L lncRNA (class in metadensity.metadensity) M main() (in module metadensity.kmer_from_read) (in module metadensity.region_call) (in module metadensity.shrink_region) make_concat_xtick() (in module metadensity.plotd) make_fixed_size() (metadensity.shrink_region.Cluster method) many_intervals() (in module metadensity.shape_from_read) mask_by_null() (in module metadensity.pos_enrich) Meta (class in metadensity.metadensity) metadensity module Metadensity (class in metadensity.metadensity) metadensity.config module metadensity.kmer_from_read module metadensity.metadensity module metadensity.plotd module metadensity.pos_enrich module metadensity.readdensity module metadensity.region_call module metadensity.sequence module metadensity.shape_from_read module metadensity.shrink_region module metadensity.truncation module MetadensityConfig (class in metadensity.config) Metagene (class in metadensity.metadensity) Metatruncate (class in metadensity.metadensity) miRNA (class in metadensity.metadensity) module metadensity metadensity.config metadensity.kmer_from_read metadensity.metadensity metadensity.plotd metadensity.pos_enrich metadensity.readdensity metadensity.region_call metadensity.sequence metadensity.shape_from_read metadensity.shrink_region metadensity.truncation multi_feature_avg() (metadensity.metadensity.Metagene method) N nan_array() (in module metadensity.metadensity) neg (metadensity.readdensity.ReadDensity.self attribute) nreads() (in module metadensity.region_call) null_thres() (in module metadensity.pos_enrich) O option_parser() (in module metadensity.region_call) order_multi_feature() (metadensity.metadensity.Metagene method) P Phastcon (class in metadensity.readdensity) plot_enrich() (in module metadensity.plotd) plot_mean_density() (in module metadensity.plotd) plot_mean_density_concat() (in module metadensity.plotd) plot_rbp_map() (in module metadensity.plotd) poission_pval() (in module metadensity.region_call) PosEnrichResult (class in metadensity.pos_enrich) Protein_coding_gene (class in metadensity.metadensity) pseudocount() (metadensity.readdensity.ReadDensity method) R read_start_sites() (in module metadensity.truncation) ReadDensity (class in metadensity.readdensity) region_based_calling() (in module metadensity.region_call) region_cluster() (in module metadensity.shrink_region) region_cluster_ri() (in module metadensity.shrink_region) remove_background() (metadensity.metadensity.Metagene method) rep_merge_options() (in module metadensity.plotd) RNU (class in metadensity.metadensity) rpm_to_r() (metadensity.readdensity.ReadDensity method) rRNA (class in metadensity.metadensity) S save_deepdish() (metadensity.metadensity.Meta method) scale_density_array() (metadensity.metadensity.Meta method) simulate_kmer_background() (in module metadensity.sequence) sites (metadensity.metadensity.circRNA.self attribute) (metadensity.metadensity.lncRNA.self attribute) (metadensity.metadensity.Metagene.self attribute) (metadensity.metadensity.miRNA.self attribute) (metadensity.metadensity.Protein_coding_gene.self attribute) (metadensity.metadensity.RNU.self attribute) (metadensity.metadensity.rRNA.self attribute) (metadensity.metadensity.snoRNA.self attribute) (metadensity.metadensity.tRNA.self attribute) (metadensity.metadensity.vaultRNA.self attribute) (metadensity.metadensity.YRNA.self attribute) snoRNA (class in metadensity.metadensity) STAMP (class in metadensity.metadensity) strand_specific_pileup() (in module metadensity.truncation) T to_bedstr() (metadensity.shrink_region.Cluster method) to_relative_axis() (metadensity.metadensity.Metagene method) total_mapped() (metadensity.readdensity.ReadDensity method) trim_or_pad() (in module metadensity.metadensity) tRNA (class in metadensity.metadensity) truncation_count() (metadensity.metadensity.Metagene method) truncation_relative_axis() (in module metadensity.truncation) truncations (metadensity.metadensity.circRNA.self attribute) (metadensity.metadensity.lncRNA.self attribute) (metadensity.metadensity.Metagene.self attribute) (metadensity.metadensity.miRNA.self attribute) (metadensity.metadensity.Protein_coding_gene.self attribute) (metadensity.metadensity.RNU.self attribute) (metadensity.metadensity.rRNA.self attribute) (metadensity.metadensity.snoRNA.self attribute) (metadensity.metadensity.tRNA.self attribute) (metadensity.metadensity.vaultRNA.self attribute) (metadensity.metadensity.YRNA.self attribute) V value (metadensity.metadensity.circRNA.self attribute) (metadensity.metadensity.lncRNA.self attribute) (metadensity.metadensity.Metagene.self attribute) (metadensity.metadensity.miRNA.self attribute) (metadensity.metadensity.Protein_coding_gene.self attribute) (metadensity.metadensity.RNU.self attribute) (metadensity.metadensity.rRNA.self attribute) (metadensity.metadensity.snoRNA.self attribute) (metadensity.metadensity.tRNA.self attribute) (metadensity.metadensity.vaultRNA.self attribute) (metadensity.metadensity.YRNA.self attribute) values() (metadensity.readdensity.Density method) (metadensity.readdensity.Phastcon method) (metadensity.readdensity.ReadDensity method) vaultRNA (class in metadensity.metadensity) W Wilcox_enrich() (in module metadensity.pos_enrich) Window (class in metadensity.metadensity) window_around() (in module metadensity.shape_from_read) window_around_eclip_sites() (in module metadensity.shape_from_read) window_feature() (metadensity.metadensity.Metagene method) windows_for_all() (in module metadensity.shape_from_read) Y YRNA (class in metadensity.metadensity)